Starting phenix.real_space_refine on Sat Jun 28 06:18:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jne_36443/06_2025/8jne_36443.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jne_36443/06_2025/8jne_36443.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jne_36443/06_2025/8jne_36443.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jne_36443/06_2025/8jne_36443.map" model { file = "/net/cci-nas-00/data/ceres_data/8jne_36443/06_2025/8jne_36443.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jne_36443/06_2025/8jne_36443.cif" } resolution = 4.68 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 309 5.49 5 S 132 5.16 5 C 19680 2.51 5 N 5946 2.21 5 O 6889 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 259 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 32956 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 614 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "C" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 835 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 720 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 819 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "G" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 805 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "H" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 714 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "I" Number of atoms: 3189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 3189 Classifications: {'DNA': 156} Link IDs: {'rna3p': 155} Chain: "J" Number of atoms: 3143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 3143 Classifications: {'DNA': 153} Link IDs: {'rna3p': 152} Chain: "K" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2163 Classifications: {'peptide': 283} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 275} Chain breaks: 2 Chain: "L" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2163 Classifications: {'peptide': 283} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 275} Chain breaks: 2 Chain: "M" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2163 Classifications: {'peptide': 283} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 275} Chain breaks: 2 Chain: "N" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1698 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 216} Chain breaks: 1 Chain: "O" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2163 Classifications: {'peptide': 283} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 275} Chain breaks: 2 Chain: "P" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2163 Classifications: {'peptide': 283} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 275} Chain breaks: 2 Chain: "Q" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2163 Classifications: {'peptide': 283} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 275} Chain breaks: 2 Chain: "R" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2163 Classifications: {'peptide': 283} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 275} Chain breaks: 2 Chain: "S" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2163 Classifications: {'peptide': 283} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 275} Chain breaks: 2 Chain: "T" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1698 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 216} Chain breaks: 1 Time building chain proxies: 18.38, per 1000 atoms: 0.56 Number of scatterers: 32956 At special positions: 0 Unit cell: (204.58, 163.24, 136.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 132 16.00 P 309 15.00 O 6889 8.00 N 5946 7.00 C 19680 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.00 Conformation dependent library (CDL) restraints added in 3.5 seconds 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6318 Finding SS restraints... Secondary structure from input PDB file: 176 helices and 20 sheets defined 57.8% alpha, 13.8% beta 142 base pairs and 288 stacking pairs defined. Time for finding SS restraints: 13.39 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.808A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 123 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 123 removed outlier: 3.755A pdb=" N SER H 123 " --> pdb=" O THR H 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 25 through 31 removed outlier: 3.703A pdb=" N GLU K 29 " --> pdb=" O ILE K 25 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLN K 30 " --> pdb=" O SER K 26 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N CYS K 31 " --> pdb=" O ARG K 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 25 through 31' Processing helix chain 'K' and resid 34 through 45 Processing helix chain 'K' and resid 48 through 54 Processing helix chain 'K' and resid 56 through 62 removed outlier: 4.358A pdb=" N LEU K 60 " --> pdb=" O PRO K 56 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 82 Processing helix chain 'K' and resid 106 through 113 Processing helix chain 'K' and resid 132 through 144 removed outlier: 3.701A pdb=" N VAL K 142 " --> pdb=" O HIS K 138 " (cutoff:3.500A) Processing helix chain 'K' and resid 145 through 146 No H-bonds generated for 'chain 'K' and resid 145 through 146' Processing helix chain 'K' and resid 147 through 151 Processing helix chain 'K' and resid 167 through 178 Processing helix chain 'K' and resid 181 through 188 Processing helix chain 'K' and resid 196 through 214 removed outlier: 3.835A pdb=" N LEU K 204 " --> pdb=" O GLN K 200 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR K 205 " --> pdb=" O THR K 201 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL K 212 " --> pdb=" O SER K 208 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU K 213 " --> pdb=" O ALA K 209 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER K 214 " --> pdb=" O MET K 210 " (cutoff:3.500A) Processing helix chain 'K' and resid 225 through 231 Processing helix chain 'K' and resid 237 through 260 Processing helix chain 'K' and resid 290 through 296 removed outlier: 4.063A pdb=" N HIS K 294 " --> pdb=" O ASN K 290 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA K 295 " --> pdb=" O ILE K 291 " (cutoff:3.500A) Processing helix chain 'L' and resid 25 through 31 removed outlier: 3.703A pdb=" N GLU L 29 " --> pdb=" O ILE L 25 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLN L 30 " --> pdb=" O SER L 26 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N CYS L 31 " --> pdb=" O ARG L 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 25 through 31' Processing helix chain 'L' and resid 34 through 45 Processing helix chain 'L' and resid 48 through 54 Processing helix chain 'L' and resid 56 through 62 removed outlier: 4.357A pdb=" N LEU L 60 " --> pdb=" O PRO L 56 " (cutoff:3.500A) Processing helix chain 'L' and resid 67 through 82 Processing helix chain 'L' and resid 106 through 113 Processing helix chain 'L' and resid 132 through 144 removed outlier: 3.701A pdb=" N VAL L 142 " --> pdb=" O HIS L 138 " (cutoff:3.500A) Processing helix chain 'L' and resid 145 through 146 No H-bonds generated for 'chain 'L' and resid 145 through 146' Processing helix chain 'L' and resid 147 through 151 Processing helix chain 'L' and resid 167 through 178 Processing helix chain 'L' and resid 181 through 188 Processing helix chain 'L' and resid 196 through 214 removed outlier: 3.835A pdb=" N LEU L 204 " --> pdb=" O GLN L 200 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR L 205 " --> pdb=" O THR L 201 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL L 212 " --> pdb=" O SER L 208 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU L 213 " --> pdb=" O ALA L 209 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER L 214 " --> pdb=" O MET L 210 " (cutoff:3.500A) Processing helix chain 'L' and resid 225 through 231 Processing helix chain 'L' and resid 237 through 260 Processing helix chain 'L' and resid 290 through 296 removed outlier: 4.062A pdb=" N HIS L 294 " --> pdb=" O ASN L 290 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA L 295 " --> pdb=" O ILE L 291 " (cutoff:3.500A) Processing helix chain 'M' and resid 25 through 31 removed outlier: 3.703A pdb=" N GLU M 29 " --> pdb=" O ILE M 25 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLN M 30 " --> pdb=" O SER M 26 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N CYS M 31 " --> pdb=" O ARG M 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 25 through 31' Processing helix chain 'M' and resid 34 through 45 Processing helix chain 'M' and resid 48 through 54 Processing helix chain 'M' and resid 56 through 62 removed outlier: 4.358A pdb=" N LEU M 60 " --> pdb=" O PRO M 56 " (cutoff:3.500A) Processing helix chain 'M' and resid 67 through 82 Processing helix chain 'M' and resid 106 through 113 Processing helix chain 'M' and resid 132 through 144 removed outlier: 3.700A pdb=" N VAL M 142 " --> pdb=" O HIS M 138 " (cutoff:3.500A) Processing helix chain 'M' and resid 145 through 146 No H-bonds generated for 'chain 'M' and resid 145 through 146' Processing helix chain 'M' and resid 147 through 151 Processing helix chain 'M' and resid 167 through 178 Processing helix chain 'M' and resid 181 through 188 Processing helix chain 'M' and resid 196 through 214 removed outlier: 3.835A pdb=" N LEU M 204 " --> pdb=" O GLN M 200 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR M 205 " --> pdb=" O THR M 201 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL M 212 " --> pdb=" O SER M 208 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU M 213 " --> pdb=" O ALA M 209 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER M 214 " --> pdb=" O MET M 210 " (cutoff:3.500A) Processing helix chain 'M' and resid 225 through 231 Processing helix chain 'M' and resid 237 through 260 Processing helix chain 'M' and resid 290 through 296 removed outlier: 4.062A pdb=" N HIS M 294 " --> pdb=" O ASN M 290 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA M 295 " --> pdb=" O ILE M 291 " (cutoff:3.500A) Processing helix chain 'N' and resid 106 through 113 Processing helix chain 'N' and resid 132 through 144 removed outlier: 3.632A pdb=" N VAL N 142 " --> pdb=" O HIS N 138 " (cutoff:3.500A) Processing helix chain 'N' and resid 145 through 146 No H-bonds generated for 'chain 'N' and resid 145 through 146' Processing helix chain 'N' and resid 147 through 151 Processing helix chain 'N' and resid 167 through 178 Processing helix chain 'N' and resid 181 through 188 Processing helix chain 'N' and resid 196 through 214 removed outlier: 3.780A pdb=" N LEU N 204 " --> pdb=" O GLN N 200 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TYR N 205 " --> pdb=" O THR N 201 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN N 206 " --> pdb=" O GLN N 202 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL N 212 " --> pdb=" O SER N 208 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLU N 213 " --> pdb=" O ALA N 209 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER N 214 " --> pdb=" O MET N 210 " (cutoff:3.500A) Processing helix chain 'N' and resid 225 through 231 removed outlier: 3.519A pdb=" N ARG N 229 " --> pdb=" O THR N 225 " (cutoff:3.500A) Processing helix chain 'N' and resid 237 through 260 Processing helix chain 'N' and resid 291 through 296 removed outlier: 3.612A pdb=" N ALA N 295 " --> pdb=" O ILE N 291 " (cutoff:3.500A) Processing helix chain 'O' and resid 25 through 31 removed outlier: 3.703A pdb=" N GLU O 29 " --> pdb=" O ILE O 25 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLN O 30 " --> pdb=" O SER O 26 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N CYS O 31 " --> pdb=" O ARG O 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 25 through 31' Processing helix chain 'O' and resid 34 through 45 Processing helix chain 'O' and resid 48 through 54 Processing helix chain 'O' and resid 56 through 62 removed outlier: 4.357A pdb=" N LEU O 60 " --> pdb=" O PRO O 56 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 82 Processing helix chain 'O' and resid 106 through 113 Processing helix chain 'O' and resid 132 through 144 removed outlier: 3.701A pdb=" N VAL O 142 " --> pdb=" O HIS O 138 " (cutoff:3.500A) Processing helix chain 'O' and resid 145 through 146 No H-bonds generated for 'chain 'O' and resid 145 through 146' Processing helix chain 'O' and resid 147 through 151 Processing helix chain 'O' and resid 167 through 178 Processing helix chain 'O' and resid 181 through 188 Processing helix chain 'O' and resid 196 through 214 removed outlier: 3.836A pdb=" N LEU O 204 " --> pdb=" O GLN O 200 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR O 205 " --> pdb=" O THR O 201 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL O 212 " --> pdb=" O SER O 208 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU O 213 " --> pdb=" O ALA O 209 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER O 214 " --> pdb=" O MET O 210 " (cutoff:3.500A) Processing helix chain 'O' and resid 225 through 231 Processing helix chain 'O' and resid 237 through 260 Processing helix chain 'O' and resid 290 through 296 removed outlier: 4.063A pdb=" N HIS O 294 " --> pdb=" O ASN O 290 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA O 295 " --> pdb=" O ILE O 291 " (cutoff:3.500A) Processing helix chain 'P' and resid 25 through 31 removed outlier: 3.703A pdb=" N GLU P 29 " --> pdb=" O ILE P 25 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLN P 30 " --> pdb=" O SER P 26 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N CYS P 31 " --> pdb=" O ARG P 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 25 through 31' Processing helix chain 'P' and resid 34 through 45 Processing helix chain 'P' and resid 48 through 54 Processing helix chain 'P' and resid 56 through 62 removed outlier: 4.358A pdb=" N LEU P 60 " --> pdb=" O PRO P 56 " (cutoff:3.500A) Processing helix chain 'P' and resid 67 through 82 Processing helix chain 'P' and resid 106 through 113 Processing helix chain 'P' and resid 132 through 144 removed outlier: 3.701A pdb=" N VAL P 142 " --> pdb=" O HIS P 138 " (cutoff:3.500A) Processing helix chain 'P' and resid 145 through 146 No H-bonds generated for 'chain 'P' and resid 145 through 146' Processing helix chain 'P' and resid 147 through 151 Processing helix chain 'P' and resid 167 through 178 Processing helix chain 'P' and resid 181 through 188 Processing helix chain 'P' and resid 196 through 214 removed outlier: 3.835A pdb=" N LEU P 204 " --> pdb=" O GLN P 200 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR P 205 " --> pdb=" O THR P 201 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL P 212 " --> pdb=" O SER P 208 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU P 213 " --> pdb=" O ALA P 209 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER P 214 " --> pdb=" O MET P 210 " (cutoff:3.500A) Processing helix chain 'P' and resid 225 through 231 Processing helix chain 'P' and resid 237 through 260 Processing helix chain 'P' and resid 290 through 296 removed outlier: 4.062A pdb=" N HIS P 294 " --> pdb=" O ASN P 290 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA P 295 " --> pdb=" O ILE P 291 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 31 removed outlier: 3.703A pdb=" N GLU Q 29 " --> pdb=" O ILE Q 25 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLN Q 30 " --> pdb=" O SER Q 26 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N CYS Q 31 " --> pdb=" O ARG Q 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 25 through 31' Processing helix chain 'Q' and resid 34 through 45 Processing helix chain 'Q' and resid 48 through 54 Processing helix chain 'Q' and resid 56 through 62 removed outlier: 4.357A pdb=" N LEU Q 60 " --> pdb=" O PRO Q 56 " (cutoff:3.500A) Processing helix chain 'Q' and resid 67 through 82 Processing helix chain 'Q' and resid 106 through 113 Processing helix chain 'Q' and resid 132 through 144 removed outlier: 3.700A pdb=" N VAL Q 142 " --> pdb=" O HIS Q 138 " (cutoff:3.500A) Processing helix chain 'Q' and resid 145 through 146 No H-bonds generated for 'chain 'Q' and resid 145 through 146' Processing helix chain 'Q' and resid 147 through 151 Processing helix chain 'Q' and resid 167 through 178 Processing helix chain 'Q' and resid 181 through 188 Processing helix chain 'Q' and resid 196 through 214 removed outlier: 3.835A pdb=" N LEU Q 204 " --> pdb=" O GLN Q 200 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR Q 205 " --> pdb=" O THR Q 201 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL Q 212 " --> pdb=" O SER Q 208 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU Q 213 " --> pdb=" O ALA Q 209 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER Q 214 " --> pdb=" O MET Q 210 " (cutoff:3.500A) Processing helix chain 'Q' and resid 225 through 231 Processing helix chain 'Q' and resid 237 through 260 Processing helix chain 'Q' and resid 290 through 296 removed outlier: 4.062A pdb=" N HIS Q 294 " --> pdb=" O ASN Q 290 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA Q 295 " --> pdb=" O ILE Q 291 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 31 removed outlier: 3.703A pdb=" N GLU R 29 " --> pdb=" O ILE R 25 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLN R 30 " --> pdb=" O SER R 26 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N CYS R 31 " --> pdb=" O ARG R 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 25 through 31' Processing helix chain 'R' and resid 34 through 45 Processing helix chain 'R' and resid 48 through 54 Processing helix chain 'R' and resid 56 through 62 removed outlier: 4.358A pdb=" N LEU R 60 " --> pdb=" O PRO R 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 82 Processing helix chain 'R' and resid 106 through 113 Processing helix chain 'R' and resid 132 through 144 removed outlier: 3.702A pdb=" N VAL R 142 " --> pdb=" O HIS R 138 " (cutoff:3.500A) Processing helix chain 'R' and resid 145 through 146 No H-bonds generated for 'chain 'R' and resid 145 through 146' Processing helix chain 'R' and resid 147 through 151 Processing helix chain 'R' and resid 167 through 178 Processing helix chain 'R' and resid 181 through 188 Processing helix chain 'R' and resid 196 through 214 removed outlier: 3.836A pdb=" N LEU R 204 " --> pdb=" O GLN R 200 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR R 205 " --> pdb=" O THR R 201 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL R 212 " --> pdb=" O SER R 208 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU R 213 " --> pdb=" O ALA R 209 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER R 214 " --> pdb=" O MET R 210 " (cutoff:3.500A) Processing helix chain 'R' and resid 225 through 231 Processing helix chain 'R' and resid 237 through 260 Processing helix chain 'R' and resid 290 through 296 removed outlier: 4.063A pdb=" N HIS R 294 " --> pdb=" O ASN R 290 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA R 295 " --> pdb=" O ILE R 291 " (cutoff:3.500A) Processing helix chain 'S' and resid 25 through 31 removed outlier: 3.703A pdb=" N GLU S 29 " --> pdb=" O ILE S 25 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLN S 30 " --> pdb=" O SER S 26 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N CYS S 31 " --> pdb=" O ARG S 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 25 through 31' Processing helix chain 'S' and resid 34 through 45 Processing helix chain 'S' and resid 48 through 54 Processing helix chain 'S' and resid 56 through 62 removed outlier: 4.358A pdb=" N LEU S 60 " --> pdb=" O PRO S 56 " (cutoff:3.500A) Processing helix chain 'S' and resid 67 through 82 Processing helix chain 'S' and resid 106 through 113 Processing helix chain 'S' and resid 132 through 144 removed outlier: 3.701A pdb=" N VAL S 142 " --> pdb=" O HIS S 138 " (cutoff:3.500A) Processing helix chain 'S' and resid 145 through 146 No H-bonds generated for 'chain 'S' and resid 145 through 146' Processing helix chain 'S' and resid 147 through 151 Processing helix chain 'S' and resid 167 through 178 Processing helix chain 'S' and resid 181 through 188 Processing helix chain 'S' and resid 196 through 214 removed outlier: 3.835A pdb=" N LEU S 204 " --> pdb=" O GLN S 200 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR S 205 " --> pdb=" O THR S 201 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL S 212 " --> pdb=" O SER S 208 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU S 213 " --> pdb=" O ALA S 209 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER S 214 " --> pdb=" O MET S 210 " (cutoff:3.500A) Processing helix chain 'S' and resid 225 through 231 Processing helix chain 'S' and resid 237 through 260 Processing helix chain 'S' and resid 290 through 296 removed outlier: 4.062A pdb=" N HIS S 294 " --> pdb=" O ASN S 290 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA S 295 " --> pdb=" O ILE S 291 " (cutoff:3.500A) Processing helix chain 'T' and resid 106 through 113 Processing helix chain 'T' and resid 132 through 144 removed outlier: 3.633A pdb=" N VAL T 142 " --> pdb=" O HIS T 138 " (cutoff:3.500A) Processing helix chain 'T' and resid 145 through 146 No H-bonds generated for 'chain 'T' and resid 145 through 146' Processing helix chain 'T' and resid 147 through 151 Processing helix chain 'T' and resid 167 through 178 Processing helix chain 'T' and resid 181 through 188 Processing helix chain 'T' and resid 196 through 214 removed outlier: 3.780A pdb=" N LEU T 204 " --> pdb=" O GLN T 200 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TYR T 205 " --> pdb=" O THR T 201 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN T 206 " --> pdb=" O GLN T 202 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL T 212 " --> pdb=" O SER T 208 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLU T 213 " --> pdb=" O ALA T 209 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER T 214 " --> pdb=" O MET T 210 " (cutoff:3.500A) Processing helix chain 'T' and resid 225 through 231 removed outlier: 3.520A pdb=" N ARG T 229 " --> pdb=" O THR T 225 " (cutoff:3.500A) Processing helix chain 'T' and resid 237 through 260 Processing helix chain 'T' and resid 291 through 296 removed outlier: 3.613A pdb=" N ALA T 295 " --> pdb=" O ILE T 291 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.865A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.902A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.975A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.761A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 6.978A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 189 through 193 removed outlier: 3.591A pdb=" N ALA K 190 " --> pdb=" O ALA K 157 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR K 159 " --> pdb=" O ALA K 190 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA K 192 " --> pdb=" O TYR K 159 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LYS K 156 " --> pdb=" O LEU K 218 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N ILE K 220 " --> pdb=" O LYS K 156 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N MET K 158 " --> pdb=" O ILE K 220 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ASP K 222 " --> pdb=" O MET K 158 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ILE K 160 " --> pdb=" O ASP K 222 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ALA K 217 " --> pdb=" O ALA K 262 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N VAL K 264 " --> pdb=" O ALA K 217 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU K 219 " --> pdb=" O VAL K 264 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N THR K 266 " --> pdb=" O LEU K 219 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N VAL K 221 " --> pdb=" O THR K 266 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE K 265 " --> pdb=" O THR K 123 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N MET K 125 " --> pdb=" O ILE K 265 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ASN K 267 " --> pdb=" O MET K 125 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLY K 127 " --> pdb=" O ASN K 267 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N ILE K 122 " --> pdb=" O THR K 298 " (cutoff:3.500A) removed outlier: 8.947A pdb=" N LEU K 300 " --> pdb=" O ILE K 122 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N GLU K 124 " --> pdb=" O LEU K 300 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N LEU K 302 " --> pdb=" O GLU K 124 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N PHE K 126 " --> pdb=" O LEU K 302 " (cutoff:3.500A) removed outlier: 9.539A pdb=" N LYS K 304 " --> pdb=" O PHE K 126 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ARG K 299 " --> pdb=" O TYR K 315 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 189 through 193 removed outlier: 3.590A pdb=" N ALA L 190 " --> pdb=" O ALA L 157 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR L 159 " --> pdb=" O ALA L 190 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA L 192 " --> pdb=" O TYR L 159 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LYS L 156 " --> pdb=" O LEU L 218 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N ILE L 220 " --> pdb=" O LYS L 156 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N MET L 158 " --> pdb=" O ILE L 220 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ASP L 222 " --> pdb=" O MET L 158 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ILE L 160 " --> pdb=" O ASP L 222 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ALA L 217 " --> pdb=" O ALA L 262 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N VAL L 264 " --> pdb=" O ALA L 217 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU L 219 " --> pdb=" O VAL L 264 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N THR L 266 " --> pdb=" O LEU L 219 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N VAL L 221 " --> pdb=" O THR L 266 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE L 265 " --> pdb=" O THR L 123 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N MET L 125 " --> pdb=" O ILE L 265 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASN L 267 " --> pdb=" O MET L 125 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLY L 127 " --> pdb=" O ASN L 267 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N ILE L 122 " --> pdb=" O THR L 298 " (cutoff:3.500A) removed outlier: 8.947A pdb=" N LEU L 300 " --> pdb=" O ILE L 122 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N GLU L 124 " --> pdb=" O LEU L 300 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N LEU L 302 " --> pdb=" O GLU L 124 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N PHE L 126 " --> pdb=" O LEU L 302 " (cutoff:3.500A) removed outlier: 9.539A pdb=" N LYS L 304 " --> pdb=" O PHE L 126 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ARG L 299 " --> pdb=" O TYR L 315 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 189 through 193 removed outlier: 3.591A pdb=" N ALA M 190 " --> pdb=" O ALA M 157 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR M 159 " --> pdb=" O ALA M 190 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA M 192 " --> pdb=" O TYR M 159 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LYS M 156 " --> pdb=" O LEU M 218 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N ILE M 220 " --> pdb=" O LYS M 156 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N MET M 158 " --> pdb=" O ILE M 220 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ASP M 222 " --> pdb=" O MET M 158 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ILE M 160 " --> pdb=" O ASP M 222 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ALA M 217 " --> pdb=" O ALA M 262 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N VAL M 264 " --> pdb=" O ALA M 217 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU M 219 " --> pdb=" O VAL M 264 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N THR M 266 " --> pdb=" O LEU M 219 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N VAL M 221 " --> pdb=" O THR M 266 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE M 265 " --> pdb=" O THR M 123 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N MET M 125 " --> pdb=" O ILE M 265 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASN M 267 " --> pdb=" O MET M 125 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLY M 127 " --> pdb=" O ASN M 267 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N ILE M 122 " --> pdb=" O THR M 298 " (cutoff:3.500A) removed outlier: 8.946A pdb=" N LEU M 300 " --> pdb=" O ILE M 122 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N GLU M 124 " --> pdb=" O LEU M 300 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N LEU M 302 " --> pdb=" O GLU M 124 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N PHE M 126 " --> pdb=" O LEU M 302 " (cutoff:3.500A) removed outlier: 9.540A pdb=" N LYS M 304 " --> pdb=" O PHE M 126 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ARG M 299 " --> pdb=" O TYR M 315 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 189 through 193 removed outlier: 6.848A pdb=" N ALA N 157 " --> pdb=" O ALA N 190 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N ALA N 192 " --> pdb=" O ALA N 157 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N TYR N 159 " --> pdb=" O ALA N 192 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LYS N 156 " --> pdb=" O LEU N 218 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N ILE N 220 " --> pdb=" O LYS N 156 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N MET N 158 " --> pdb=" O ILE N 220 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ASP N 222 " --> pdb=" O MET N 158 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ILE N 160 " --> pdb=" O ASP N 222 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ALA N 217 " --> pdb=" O ALA N 262 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N VAL N 264 " --> pdb=" O ALA N 217 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU N 219 " --> pdb=" O VAL N 264 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N THR N 266 " --> pdb=" O LEU N 219 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N VAL N 221 " --> pdb=" O THR N 266 " (cutoff:3.500A) removed outlier: 9.157A pdb=" N GLN N 268 " --> pdb=" O VAL N 221 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ILE N 122 " --> pdb=" O THR N 298 " (cutoff:3.500A) removed outlier: 9.144A pdb=" N LEU N 300 " --> pdb=" O ILE N 122 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N GLU N 124 " --> pdb=" O LEU N 300 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N LEU N 302 " --> pdb=" O GLU N 124 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N PHE N 126 " --> pdb=" O LEU N 302 " (cutoff:3.500A) removed outlier: 9.478A pdb=" N LYS N 304 " --> pdb=" O PHE N 126 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N ARG N 299 " --> pdb=" O TYR N 315 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TYR N 315 " --> pdb=" O ARG N 299 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'O' and resid 189 through 193 removed outlier: 3.590A pdb=" N ALA O 190 " --> pdb=" O ALA O 157 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR O 159 " --> pdb=" O ALA O 190 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA O 192 " --> pdb=" O TYR O 159 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LYS O 156 " --> pdb=" O LEU O 218 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N ILE O 220 " --> pdb=" O LYS O 156 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N MET O 158 " --> pdb=" O ILE O 220 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ASP O 222 " --> pdb=" O MET O 158 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ILE O 160 " --> pdb=" O ASP O 222 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ALA O 217 " --> pdb=" O ALA O 262 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N VAL O 264 " --> pdb=" O ALA O 217 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU O 219 " --> pdb=" O VAL O 264 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N THR O 266 " --> pdb=" O LEU O 219 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N VAL O 221 " --> pdb=" O THR O 266 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ILE O 265 " --> pdb=" O THR O 123 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N MET O 125 " --> pdb=" O ILE O 265 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ASN O 267 " --> pdb=" O MET O 125 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLY O 127 " --> pdb=" O ASN O 267 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N ILE O 122 " --> pdb=" O THR O 298 " (cutoff:3.500A) removed outlier: 8.947A pdb=" N LEU O 300 " --> pdb=" O ILE O 122 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N GLU O 124 " --> pdb=" O LEU O 300 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N LEU O 302 " --> pdb=" O GLU O 124 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N PHE O 126 " --> pdb=" O LEU O 302 " (cutoff:3.500A) removed outlier: 9.539A pdb=" N LYS O 304 " --> pdb=" O PHE O 126 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ARG O 299 " --> pdb=" O TYR O 315 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'P' and resid 189 through 193 removed outlier: 3.591A pdb=" N ALA P 190 " --> pdb=" O ALA P 157 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR P 159 " --> pdb=" O ALA P 190 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA P 192 " --> pdb=" O TYR P 159 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LYS P 156 " --> pdb=" O LEU P 218 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N ILE P 220 " --> pdb=" O LYS P 156 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N MET P 158 " --> pdb=" O ILE P 220 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N ASP P 222 " --> pdb=" O MET P 158 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ILE P 160 " --> pdb=" O ASP P 222 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ALA P 217 " --> pdb=" O ALA P 262 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N VAL P 264 " --> pdb=" O ALA P 217 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU P 219 " --> pdb=" O VAL P 264 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N THR P 266 " --> pdb=" O LEU P 219 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N VAL P 221 " --> pdb=" O THR P 266 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE P 265 " --> pdb=" O THR P 123 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N MET P 125 " --> pdb=" O ILE P 265 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ASN P 267 " --> pdb=" O MET P 125 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLY P 127 " --> pdb=" O ASN P 267 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N ILE P 122 " --> pdb=" O THR P 298 " (cutoff:3.500A) removed outlier: 8.947A pdb=" N LEU P 300 " --> pdb=" O ILE P 122 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N GLU P 124 " --> pdb=" O LEU P 300 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N LEU P 302 " --> pdb=" O GLU P 124 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N PHE P 126 " --> pdb=" O LEU P 302 " (cutoff:3.500A) removed outlier: 9.539A pdb=" N LYS P 304 " --> pdb=" O PHE P 126 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ARG P 299 " --> pdb=" O TYR P 315 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'Q' and resid 189 through 193 removed outlier: 3.590A pdb=" N ALA Q 190 " --> pdb=" O ALA Q 157 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR Q 159 " --> pdb=" O ALA Q 190 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA Q 192 " --> pdb=" O TYR Q 159 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LYS Q 156 " --> pdb=" O LEU Q 218 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N ILE Q 220 " --> pdb=" O LYS Q 156 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N MET Q 158 " --> pdb=" O ILE Q 220 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ASP Q 222 " --> pdb=" O MET Q 158 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ILE Q 160 " --> pdb=" O ASP Q 222 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ALA Q 217 " --> pdb=" O ALA Q 262 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N VAL Q 264 " --> pdb=" O ALA Q 217 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU Q 219 " --> pdb=" O VAL Q 264 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N THR Q 266 " --> pdb=" O LEU Q 219 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N VAL Q 221 " --> pdb=" O THR Q 266 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE Q 265 " --> pdb=" O THR Q 123 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N MET Q 125 " --> pdb=" O ILE Q 265 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASN Q 267 " --> pdb=" O MET Q 125 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLY Q 127 " --> pdb=" O ASN Q 267 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N ILE Q 122 " --> pdb=" O THR Q 298 " (cutoff:3.500A) removed outlier: 8.947A pdb=" N LEU Q 300 " --> pdb=" O ILE Q 122 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N GLU Q 124 " --> pdb=" O LEU Q 300 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N LEU Q 302 " --> pdb=" O GLU Q 124 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N PHE Q 126 " --> pdb=" O LEU Q 302 " (cutoff:3.500A) removed outlier: 9.539A pdb=" N LYS Q 304 " --> pdb=" O PHE Q 126 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ARG Q 299 " --> pdb=" O TYR Q 315 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'R' and resid 189 through 193 removed outlier: 3.590A pdb=" N ALA R 190 " --> pdb=" O ALA R 157 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR R 159 " --> pdb=" O ALA R 190 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA R 192 " --> pdb=" O TYR R 159 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LYS R 156 " --> pdb=" O LEU R 218 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N ILE R 220 " --> pdb=" O LYS R 156 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N MET R 158 " --> pdb=" O ILE R 220 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ASP R 222 " --> pdb=" O MET R 158 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ILE R 160 " --> pdb=" O ASP R 222 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ALA R 217 " --> pdb=" O ALA R 262 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N VAL R 264 " --> pdb=" O ALA R 217 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU R 219 " --> pdb=" O VAL R 264 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N THR R 266 " --> pdb=" O LEU R 219 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N VAL R 221 " --> pdb=" O THR R 266 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ILE R 265 " --> pdb=" O THR R 123 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N MET R 125 " --> pdb=" O ILE R 265 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASN R 267 " --> pdb=" O MET R 125 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLY R 127 " --> pdb=" O ASN R 267 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N ILE R 122 " --> pdb=" O THR R 298 " (cutoff:3.500A) removed outlier: 8.947A pdb=" N LEU R 300 " --> pdb=" O ILE R 122 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N GLU R 124 " --> pdb=" O LEU R 300 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N LEU R 302 " --> pdb=" O GLU R 124 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N PHE R 126 " --> pdb=" O LEU R 302 " (cutoff:3.500A) removed outlier: 9.539A pdb=" N LYS R 304 " --> pdb=" O PHE R 126 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ARG R 299 " --> pdb=" O TYR R 315 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'S' and resid 189 through 193 removed outlier: 3.591A pdb=" N ALA S 190 " --> pdb=" O ALA S 157 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR S 159 " --> pdb=" O ALA S 190 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA S 192 " --> pdb=" O TYR S 159 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LYS S 156 " --> pdb=" O LEU S 218 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N ILE S 220 " --> pdb=" O LYS S 156 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N MET S 158 " --> pdb=" O ILE S 220 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ASP S 222 " --> pdb=" O MET S 158 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ILE S 160 " --> pdb=" O ASP S 222 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ALA S 217 " --> pdb=" O ALA S 262 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N VAL S 264 " --> pdb=" O ALA S 217 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU S 219 " --> pdb=" O VAL S 264 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N THR S 266 " --> pdb=" O LEU S 219 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N VAL S 221 " --> pdb=" O THR S 266 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE S 265 " --> pdb=" O THR S 123 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N MET S 125 " --> pdb=" O ILE S 265 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ASN S 267 " --> pdb=" O MET S 125 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLY S 127 " --> pdb=" O ASN S 267 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N ILE S 122 " --> pdb=" O THR S 298 " (cutoff:3.500A) removed outlier: 8.947A pdb=" N LEU S 300 " --> pdb=" O ILE S 122 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N GLU S 124 " --> pdb=" O LEU S 300 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N LEU S 302 " --> pdb=" O GLU S 124 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N PHE S 126 " --> pdb=" O LEU S 302 " (cutoff:3.500A) removed outlier: 9.540A pdb=" N LYS S 304 " --> pdb=" O PHE S 126 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ARG S 299 " --> pdb=" O TYR S 315 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'T' and resid 189 through 193 removed outlier: 6.849A pdb=" N ALA T 157 " --> pdb=" O ALA T 190 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N ALA T 192 " --> pdb=" O ALA T 157 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N TYR T 159 " --> pdb=" O ALA T 192 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LYS T 156 " --> pdb=" O LEU T 218 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N ILE T 220 " --> pdb=" O LYS T 156 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N MET T 158 " --> pdb=" O ILE T 220 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ASP T 222 " --> pdb=" O MET T 158 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ILE T 160 " --> pdb=" O ASP T 222 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ALA T 217 " --> pdb=" O ALA T 262 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N VAL T 264 " --> pdb=" O ALA T 217 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU T 219 " --> pdb=" O VAL T 264 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N THR T 266 " --> pdb=" O LEU T 219 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N VAL T 221 " --> pdb=" O THR T 266 " (cutoff:3.500A) removed outlier: 9.157A pdb=" N GLN T 268 " --> pdb=" O VAL T 221 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ILE T 122 " --> pdb=" O THR T 298 " (cutoff:3.500A) removed outlier: 9.144A pdb=" N LEU T 300 " --> pdb=" O ILE T 122 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N GLU T 124 " --> pdb=" O LEU T 300 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N LEU T 302 " --> pdb=" O GLU T 124 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N PHE T 126 " --> pdb=" O LEU T 302 " (cutoff:3.500A) removed outlier: 9.478A pdb=" N LYS T 304 " --> pdb=" O PHE T 126 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N ARG T 299 " --> pdb=" O TYR T 315 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TYR T 315 " --> pdb=" O ARG T 299 " (cutoff:3.500A) 1348 hydrogen bonds defined for protein. 3957 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 363 hydrogen bonds 722 hydrogen bond angles 0 basepair planarities 142 basepair parallelities 288 stacking parallelities Total time for adding SS restraints: 13.33 Time building geometry restraints manager: 9.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10204 1.34 - 1.47: 9005 1.47 - 1.59: 14037 1.59 - 1.72: 608 1.72 - 1.84: 212 Bond restraints: 34066 Sorted by residual: bond pdb=" N MET N 243 " pdb=" CA MET N 243 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.28e-02 6.10e+03 5.52e+00 bond pdb=" C GLU E 73 " pdb=" O GLU E 73 " ideal model delta sigma weight residual 1.236 1.262 -0.026 1.15e-02 7.56e+03 5.07e+00 bond pdb=" CA VAL E 117 " pdb=" CB VAL E 117 " ideal model delta sigma weight residual 1.542 1.566 -0.024 1.08e-02 8.57e+03 4.88e+00 bond pdb=" P DT J 14 " pdb=" OP2 DT J 14 " ideal model delta sigma weight residual 1.480 1.521 -0.041 2.00e-02 2.50e+03 4.26e+00 bond pdb=" C GLU G 61 " pdb=" O GLU G 61 " ideal model delta sigma weight residual 1.237 1.261 -0.024 1.16e-02 7.43e+03 4.25e+00 ... (remaining 34061 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 45439 2.46 - 4.92: 1659 4.92 - 7.38: 136 7.38 - 9.83: 26 9.83 - 12.29: 10 Bond angle restraints: 47270 Sorted by residual: angle pdb=" N VAL E 117 " pdb=" CA VAL E 117 " pdb=" C VAL E 117 " ideal model delta sigma weight residual 113.10 107.09 6.01 9.70e-01 1.06e+00 3.84e+01 angle pdb=" C HIS A 39 " pdb=" CA HIS A 39 " pdb=" CB HIS A 39 " ideal model delta sigma weight residual 109.51 117.71 -8.20 1.71e+00 3.42e-01 2.30e+01 angle pdb=" C HIS D 49 " pdb=" N PRO D 50 " pdb=" CA PRO D 50 " ideal model delta sigma weight residual 119.47 124.93 -5.46 1.16e+00 7.43e-01 2.22e+01 angle pdb=" N PHE T 195 " pdb=" CA PHE T 195 " pdb=" CB PHE T 195 " ideal model delta sigma weight residual 110.44 103.22 7.22 1.56e+00 4.11e-01 2.14e+01 angle pdb=" N PHE N 195 " pdb=" CA PHE N 195 " pdb=" CB PHE N 195 " ideal model delta sigma weight residual 110.44 103.23 7.21 1.56e+00 4.11e-01 2.14e+01 ... (remaining 47265 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.87: 16575 18.87 - 37.74: 1652 37.74 - 56.60: 1354 56.60 - 75.47: 218 75.47 - 94.34: 31 Dihedral angle restraints: 19830 sinusoidal: 9968 harmonic: 9862 Sorted by residual: dihedral pdb=" CA VAL R 334 " pdb=" C VAL R 334 " pdb=" N GLY R 335 " pdb=" CA GLY R 335 " ideal model delta harmonic sigma weight residual -180.00 -154.42 -25.58 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA VAL S 334 " pdb=" C VAL S 334 " pdb=" N GLY S 335 " pdb=" CA GLY S 335 " ideal model delta harmonic sigma weight residual -180.00 -154.43 -25.57 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA VAL L 334 " pdb=" C VAL L 334 " pdb=" N GLY L 335 " pdb=" CA GLY L 335 " ideal model delta harmonic sigma weight residual -180.00 -154.44 -25.56 0 5.00e+00 4.00e-02 2.61e+01 ... (remaining 19827 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 5318 0.128 - 0.256: 67 0.256 - 0.384: 1 0.384 - 0.512: 8 0.512 - 0.640: 21 Chirality restraints: 5415 Sorted by residual: chirality pdb=" P DT J 1 " pdb=" OP1 DT J 1 " pdb=" OP2 DT J 1 " pdb=" O5' DT J 1 " both_signs ideal model delta sigma weight residual True 2.35 -2.99 -0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" P DT J 14 " pdb=" OP1 DT J 14 " pdb=" OP2 DT J 14 " pdb=" O5' DT J 14 " both_signs ideal model delta sigma weight residual True 2.35 -2.95 -0.60 2.00e-01 2.50e+01 9.06e+00 chirality pdb=" P DA I 153 " pdb=" OP1 DA I 153 " pdb=" OP2 DA I 153 " pdb=" O5' DA I 153 " both_signs ideal model delta sigma weight residual True 2.35 -2.94 -0.60 2.00e-01 2.50e+01 8.97e+00 ... (remaining 5412 not shown) Planarity restraints: 5012 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE T 195 " -0.062 2.00e-02 2.50e+03 4.48e-02 3.52e+01 pdb=" CG PHE T 195 " 0.096 2.00e-02 2.50e+03 pdb=" CD1 PHE T 195 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE T 195 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE T 195 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE T 195 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE T 195 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE N 195 " 0.062 2.00e-02 2.50e+03 4.48e-02 3.52e+01 pdb=" CG PHE N 195 " -0.096 2.00e-02 2.50e+03 pdb=" CD1 PHE N 195 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE N 195 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE N 195 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE N 195 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE N 195 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 39 " -0.043 2.00e-02 2.50e+03 3.57e-02 1.91e+01 pdb=" CG HIS A 39 " 0.058 2.00e-02 2.50e+03 pdb=" ND1 HIS A 39 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS A 39 " 0.024 2.00e-02 2.50e+03 pdb=" CE1 HIS A 39 " 0.004 2.00e-02 2.50e+03 pdb=" NE2 HIS A 39 " -0.044 2.00e-02 2.50e+03 ... (remaining 5009 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 172 2.41 - 3.03: 20447 3.03 - 3.66: 56082 3.66 - 4.28: 87165 4.28 - 4.90: 132621 Nonbonded interactions: 296487 Sorted by model distance: nonbonded pdb=" NH1 ARG E 72 " pdb=" OP1 DC I 50 " model vdw 1.788 3.120 nonbonded pdb=" OH TYR H 42 " pdb=" O5' DG I 20 " model vdw 1.818 3.040 nonbonded pdb=" NH2 ARG C 20 " pdb=" OP1 DG J 39 " model vdw 1.851 3.120 nonbonded pdb=" NH2 ARG E 72 " pdb=" OP2 DC I 50 " model vdw 1.876 3.120 nonbonded pdb=" OG1 THR G 76 " pdb=" C3' DG J 138 " model vdw 1.905 3.470 ... (remaining 296482 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and resid 38 through 133) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 25 through 101) } ncs_group { reference = (chain 'C' and resid 15 through 118) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 33 through 123) selection = chain 'H' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' } ncs_group { reference = chain 'N' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.260 Check model and map are aligned: 0.230 Set scattering table: 0.290 Process input model: 80.070 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6802 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 34066 Z= 0.302 Angle : 1.093 12.292 47270 Z= 0.678 Chirality : 0.063 0.640 5415 Planarity : 0.006 0.089 5012 Dihedral : 20.643 94.338 13512 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 24.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Rotamer: Outliers : 0.14 % Allowed : 0.79 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.13), residues: 3380 helix: 0.03 (0.11), residues: 1697 sheet: 0.30 (0.20), residues: 542 loop : -0.25 (0.17), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.030 0.002 HIS T 294 PHE 0.096 0.003 PHE N 195 TYR 0.016 0.003 TYR F 51 ARG 0.021 0.002 ARG N 299 Details of bonding type rmsd hydrogen bonds : bond 0.20823 ( 1711) hydrogen bonds : angle 6.82401 ( 4679) covalent geometry : bond 0.00587 (34066) covalent geometry : angle 1.09304 (47270) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 352 time to evaluate : 3.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8059 (mt) cc_final: 0.7680 (mp) REVERT: A 61 LEU cc_start: 0.7677 (mt) cc_final: 0.7439 (mt) REVERT: A 74 ILE cc_start: 0.9526 (mt) cc_final: 0.9318 (mm) REVERT: A 106 ASP cc_start: 0.9045 (m-30) cc_final: 0.8500 (m-30) REVERT: B 46 ILE cc_start: 0.9438 (mt) cc_final: 0.9128 (tp) REVERT: B 68 ASP cc_start: 0.8931 (m-30) cc_final: 0.8660 (m-30) REVERT: B 81 VAL cc_start: 0.9020 (t) cc_final: 0.8771 (t) REVERT: B 96 THR cc_start: 0.9038 (m) cc_final: 0.8738 (p) REVERT: D 37 TYR cc_start: 0.8137 (m-80) cc_final: 0.7621 (m-80) REVERT: D 54 ILE cc_start: 0.8586 (tt) cc_final: 0.8332 (tt) REVERT: D 62 MET cc_start: 0.8330 (mmm) cc_final: 0.8121 (mmm) REVERT: D 106 LEU cc_start: 0.8866 (tp) cc_final: 0.8521 (mt) REVERT: E 54 TYR cc_start: 0.8426 (m-80) cc_final: 0.7960 (m-10) REVERT: E 94 GLU cc_start: 0.8659 (mm-30) cc_final: 0.8184 (mm-30) REVERT: E 99 TYR cc_start: 0.8394 (t80) cc_final: 0.8139 (t80) REVERT: E 119 ILE cc_start: 0.9374 (pt) cc_final: 0.8873 (pt) REVERT: E 124 ILE cc_start: 0.9515 (mt) cc_final: 0.9176 (mm) REVERT: F 44 LYS cc_start: 0.9022 (tttt) cc_final: 0.8518 (mtpp) REVERT: F 46 ILE cc_start: 0.9154 (mt) cc_final: 0.8880 (tt) REVERT: F 81 VAL cc_start: 0.8462 (t) cc_final: 0.8070 (t) REVERT: F 85 ASP cc_start: 0.8538 (m-30) cc_final: 0.8298 (m-30) REVERT: G 114 VAL cc_start: 0.8434 (t) cc_final: 0.8091 (p) REVERT: G 115 LEU cc_start: 0.8884 (mt) cc_final: 0.8167 (mp) REVERT: H 37 TYR cc_start: 0.7981 (m-80) cc_final: 0.7710 (m-10) REVERT: H 61 ILE cc_start: 0.9678 (mt) cc_final: 0.9306 (mm) REVERT: H 65 PHE cc_start: 0.8983 (t80) cc_final: 0.8713 (t80) REVERT: H 73 ILE cc_start: 0.9790 (mt) cc_final: 0.9580 (tp) REVERT: H 100 LEU cc_start: 0.9236 (mt) cc_final: 0.9033 (mt) REVERT: K 326 MET cc_start: 0.3037 (tpt) cc_final: 0.2614 (tpt) REVERT: L 50 GLU cc_start: 0.7985 (tt0) cc_final: 0.7408 (tt0) REVERT: L 210 MET cc_start: 0.2391 (tmm) cc_final: 0.0943 (ppp) REVERT: L 211 MET cc_start: 0.2829 (ttm) cc_final: 0.2420 (ttm) REVERT: L 254 ARG cc_start: 0.1415 (ttm170) cc_final: 0.0887 (ptt-90) REVERT: L 326 MET cc_start: 0.2701 (tpt) cc_final: 0.1694 (ptm) REVERT: M 30 GLN cc_start: 0.4970 (mp10) cc_final: 0.4354 (tm-30) REVERT: M 235 ARG cc_start: -0.0296 (mmt180) cc_final: -0.0591 (mpt180) REVERT: N 210 MET cc_start: 0.2131 (tmm) cc_final: 0.1833 (tmm) REVERT: S 210 MET cc_start: 0.4584 (tmm) cc_final: 0.3221 (ppp) REVERT: S 243 MET cc_start: 0.6316 (mmt) cc_final: 0.5907 (ppp) REVERT: T 306 ARG cc_start: 0.2747 (mmm160) cc_final: 0.1930 (tpt170) outliers start: 4 outliers final: 1 residues processed: 353 average time/residue: 0.4783 time to fit residues: 265.6189 Evaluate side-chains 183 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 182 time to evaluate : 2.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 310 optimal weight: 5.9990 chunk 278 optimal weight: 6.9990 chunk 154 optimal weight: 8.9990 chunk 95 optimal weight: 7.9990 chunk 188 optimal weight: 10.0000 chunk 149 optimal weight: 10.0000 chunk 288 optimal weight: 10.0000 chunk 111 optimal weight: 20.0000 chunk 175 optimal weight: 30.0000 chunk 214 optimal weight: 0.7980 chunk 334 optimal weight: 8.9990 overall best weight: 6.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS B 93 GLN D 49 HIS E 39 HIS E 108 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 244 HIS ** L 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 202 GLN ** N 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 294 HIS ** Q 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 114 GLN T 206 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.062626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.047367 restraints weight = 373362.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.046837 restraints weight = 308217.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.046875 restraints weight = 233223.866| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 34066 Z= 0.245 Angle : 0.712 10.845 47270 Z= 0.393 Chirality : 0.044 0.245 5415 Planarity : 0.006 0.079 5012 Dihedral : 25.103 97.425 7175 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 19.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 0.07 % Allowed : 3.64 % Favored : 96.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.14), residues: 3380 helix: 0.73 (0.12), residues: 1746 sheet: 0.83 (0.27), residues: 342 loop : -0.74 (0.16), residues: 1292 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.002 HIS K 244 PHE 0.022 0.002 PHE N 195 TYR 0.028 0.002 TYR O 54 ARG 0.008 0.001 ARG M 170 Details of bonding type rmsd hydrogen bonds : bond 0.06443 ( 1711) hydrogen bonds : angle 4.93675 ( 4679) covalent geometry : bond 0.00524 (34066) covalent geometry : angle 0.71175 (47270) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 206 time to evaluate : 3.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 CYS cc_start: 0.9226 (m) cc_final: 0.8936 (t) REVERT: A 125 GLN cc_start: 0.9099 (mp10) cc_final: 0.8764 (mm-40) REVERT: B 68 ASP cc_start: 0.9030 (m-30) cc_final: 0.8719 (m-30) REVERT: C 101 THR cc_start: 0.9347 (m) cc_final: 0.9128 (p) REVERT: D 62 MET cc_start: 0.9194 (mmm) cc_final: 0.8807 (mmm) REVERT: D 68 ASP cc_start: 0.9364 (t70) cc_final: 0.8981 (t0) REVERT: D 69 ILE cc_start: 0.9589 (mm) cc_final: 0.9210 (tp) REVERT: E 54 TYR cc_start: 0.8599 (m-80) cc_final: 0.8248 (m-10) REVERT: E 94 GLU cc_start: 0.9069 (mm-30) cc_final: 0.8761 (mm-30) REVERT: E 105 GLU cc_start: 0.8771 (tm-30) cc_final: 0.8423 (tm-30) REVERT: E 119 ILE cc_start: 0.9362 (pt) cc_final: 0.8893 (pt) REVERT: E 120 MET cc_start: 0.7974 (mpp) cc_final: 0.7714 (mpp) REVERT: E 130 ILE cc_start: 0.9637 (mt) cc_final: 0.8953 (mt) REVERT: F 81 VAL cc_start: 0.8625 (t) cc_final: 0.8260 (t) REVERT: F 85 ASP cc_start: 0.8954 (m-30) cc_final: 0.8698 (m-30) REVERT: F 98 TYR cc_start: 0.8325 (m-80) cc_final: 0.8123 (m-80) REVERT: G 51 LEU cc_start: 0.9837 (tp) cc_final: 0.9530 (tp) REVERT: G 55 LEU cc_start: 0.9842 (mt) cc_final: 0.9565 (mt) REVERT: G 110 ASN cc_start: 0.9178 (m-40) cc_final: 0.8923 (m110) REVERT: G 112 GLN cc_start: 0.7299 (mm-40) cc_final: 0.7003 (tm-30) REVERT: G 114 VAL cc_start: 0.8462 (t) cc_final: 0.8184 (t) REVERT: H 61 ILE cc_start: 0.9740 (mt) cc_final: 0.9449 (mt) REVERT: K 158 MET cc_start: -0.2000 (mmm) cc_final: -0.2346 (mmm) REVERT: K 210 MET cc_start: 0.6659 (tmm) cc_final: 0.6247 (ppp) REVERT: K 326 MET cc_start: 0.4583 (tpt) cc_final: 0.4183 (tpt) REVERT: L 125 MET cc_start: 0.4656 (pmm) cc_final: 0.4157 (ptm) REVERT: L 326 MET cc_start: 0.1249 (tpt) cc_final: 0.0997 (ptp) REVERT: M 30 GLN cc_start: 0.5307 (mp10) cc_final: 0.4562 (tm-30) REVERT: M 210 MET cc_start: 0.1798 (ppp) cc_final: 0.1235 (ptm) REVERT: M 211 MET cc_start: -0.1414 (ttm) cc_final: -0.1755 (ttt) REVERT: P 326 MET cc_start: 0.7262 (mmp) cc_final: 0.6843 (mmp) REVERT: R 158 MET cc_start: 0.3157 (mmm) cc_final: 0.2727 (mmp) REVERT: R 210 MET cc_start: -0.1811 (tmm) cc_final: -0.2630 (tmm) REVERT: R 235 ARG cc_start: 0.1585 (mmt180) cc_final: -0.0931 (ptt180) REVERT: S 34 ASN cc_start: 0.6238 (p0) cc_final: 0.6034 (p0) REVERT: S 243 MET cc_start: 0.6231 (mmt) cc_final: 0.5667 (ppp) REVERT: S 326 MET cc_start: 0.5203 (mpp) cc_final: 0.4990 (mpp) REVERT: T 306 ARG cc_start: 0.2405 (mmm160) cc_final: 0.2197 (tpt170) outliers start: 2 outliers final: 0 residues processed: 208 average time/residue: 0.4521 time to fit residues: 154.1881 Evaluate side-chains 151 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 3.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 202 optimal weight: 30.0000 chunk 98 optimal weight: 10.0000 chunk 89 optimal weight: 8.9990 chunk 86 optimal weight: 10.0000 chunk 296 optimal weight: 7.9990 chunk 340 optimal weight: 10.0000 chunk 103 optimal weight: 0.9980 chunk 185 optimal weight: 6.9990 chunk 38 optimal weight: 0.0980 chunk 267 optimal weight: 8.9990 chunk 183 optimal weight: 1.9990 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** L 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 206 GLN ** P 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 62 ASN Q 294 HIS ** R 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.062183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.042878 restraints weight = 398516.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.044278 restraints weight = 207696.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.045155 restraints weight = 133029.058| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.4472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 34066 Z= 0.162 Angle : 0.571 7.703 47270 Z= 0.323 Chirality : 0.039 0.274 5415 Planarity : 0.004 0.054 5012 Dihedral : 24.972 101.537 7175 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.14), residues: 3380 helix: 1.02 (0.12), residues: 1804 sheet: 0.37 (0.23), residues: 480 loop : -0.46 (0.18), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS B 75 PHE 0.023 0.002 PHE E 104 TYR 0.031 0.002 TYR H 40 ARG 0.006 0.000 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.04569 ( 1711) hydrogen bonds : angle 4.29595 ( 4679) covalent geometry : bond 0.00342 (34066) covalent geometry : angle 0.57144 (47270) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 5.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8184 (mmm) cc_final: 0.7658 (mmm) REVERT: A 125 GLN cc_start: 0.9096 (mp10) cc_final: 0.8732 (mm-40) REVERT: B 68 ASP cc_start: 0.9339 (m-30) cc_final: 0.9031 (m-30) REVERT: C 101 THR cc_start: 0.9234 (m) cc_final: 0.8953 (p) REVERT: D 62 MET cc_start: 0.9546 (mmm) cc_final: 0.9211 (mmm) REVERT: E 54 TYR cc_start: 0.8659 (m-80) cc_final: 0.8262 (m-10) REVERT: E 105 GLU cc_start: 0.9203 (tm-30) cc_final: 0.8869 (tm-30) REVERT: E 110 CYS cc_start: 0.9613 (m) cc_final: 0.9250 (p) REVERT: E 119 ILE cc_start: 0.9333 (pt) cc_final: 0.8933 (pt) REVERT: E 120 MET cc_start: 0.8209 (mpp) cc_final: 0.7759 (mpp) REVERT: F 44 LYS cc_start: 0.8918 (ttmm) cc_final: 0.8654 (tppp) REVERT: F 81 VAL cc_start: 0.8841 (t) cc_final: 0.8550 (t) REVERT: F 84 MET cc_start: 0.8803 (mmt) cc_final: 0.8476 (mmt) REVERT: F 85 ASP cc_start: 0.8948 (m-30) cc_final: 0.8681 (m-30) REVERT: G 51 LEU cc_start: 0.9797 (tp) cc_final: 0.9457 (tp) REVERT: G 55 LEU cc_start: 0.9855 (mt) cc_final: 0.9550 (mt) REVERT: G 91 GLU cc_start: 0.8692 (pp20) cc_final: 0.8427 (tm-30) REVERT: G 110 ASN cc_start: 0.9291 (m-40) cc_final: 0.8983 (m110) REVERT: G 112 GLN cc_start: 0.7364 (mm-40) cc_final: 0.6902 (tm-30) REVERT: G 114 VAL cc_start: 0.8584 (t) cc_final: 0.8338 (t) REVERT: H 35 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7544 (pm20) REVERT: H 61 ILE cc_start: 0.9763 (mt) cc_final: 0.9563 (mt) REVERT: H 64 SER cc_start: 0.9422 (m) cc_final: 0.8972 (t) REVERT: K 211 MET cc_start: -0.0679 (ttp) cc_final: -0.0974 (ttm) REVERT: K 326 MET cc_start: 0.4771 (tpt) cc_final: 0.4381 (tpp) REVERT: L 158 MET cc_start: 0.4460 (mmp) cc_final: 0.3749 (mmt) REVERT: M 30 GLN cc_start: 0.5837 (mp10) cc_final: 0.5323 (tm-30) REVERT: M 210 MET cc_start: 0.3191 (ppp) cc_final: 0.2757 (ptm) REVERT: M 211 MET cc_start: 0.1014 (ttm) cc_final: 0.0804 (ttt) REVERT: R 210 MET cc_start: -0.1181 (tmm) cc_final: -0.1921 (tmm) REVERT: S 243 MET cc_start: 0.6183 (mmt) cc_final: 0.5771 (ppp) REVERT: T 306 ARG cc_start: 0.2619 (mmm160) cc_final: 0.2282 (tpt170) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.5350 time to fit residues: 167.5831 Evaluate side-chains 138 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 2.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 175 optimal weight: 50.0000 chunk 295 optimal weight: 7.9990 chunk 259 optimal weight: 9.9990 chunk 179 optimal weight: 40.0000 chunk 227 optimal weight: 7.9990 chunk 27 optimal weight: 10.0000 chunk 273 optimal weight: 9.9990 chunk 6 optimal weight: 1.9990 chunk 348 optimal weight: 50.0000 chunk 275 optimal weight: 7.9990 chunk 207 optimal weight: 9.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN C 24 GLN E 108 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 267 ASN ** R 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.058525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.043215 restraints weight = 376681.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.041986 restraints weight = 336420.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.042352 restraints weight = 226478.374| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.6014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 34066 Z= 0.254 Angle : 0.668 11.367 47270 Z= 0.371 Chirality : 0.042 0.232 5415 Planarity : 0.005 0.056 5012 Dihedral : 25.435 104.680 7175 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 19.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.04 % Allowed : 2.09 % Favored : 97.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.14), residues: 3380 helix: 0.74 (0.12), residues: 1748 sheet: 0.34 (0.22), residues: 490 loop : -0.21 (0.18), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.001 HIS B 75 PHE 0.026 0.002 PHE E 104 TYR 0.030 0.002 TYR H 40 ARG 0.043 0.001 ARG B 92 Details of bonding type rmsd hydrogen bonds : bond 0.06968 ( 1711) hydrogen bonds : angle 4.61853 ( 4679) covalent geometry : bond 0.00547 (34066) covalent geometry : angle 0.66821 (47270) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 159 time to evaluate : 3.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8231 (mmm) cc_final: 0.7862 (mmm) REVERT: A 125 GLN cc_start: 0.9141 (mp10) cc_final: 0.8710 (mm110) REVERT: B 68 ASP cc_start: 0.9214 (m-30) cc_final: 0.8355 (t70) REVERT: B 92 ARG cc_start: 0.8900 (tmm160) cc_final: 0.8648 (ttp80) REVERT: D 62 MET cc_start: 0.9435 (mmm) cc_final: 0.9016 (mmm) REVERT: E 54 TYR cc_start: 0.8601 (m-80) cc_final: 0.8212 (m-10) REVERT: F 81 VAL cc_start: 0.8729 (t) cc_final: 0.8524 (t) REVERT: G 91 GLU cc_start: 0.8833 (pp20) cc_final: 0.8545 (tm-30) REVERT: G 112 GLN cc_start: 0.7718 (mm-40) cc_final: 0.7206 (tm-30) REVERT: H 64 SER cc_start: 0.9478 (m) cc_final: 0.9241 (p) REVERT: H 80 LEU cc_start: 0.9615 (mt) cc_final: 0.8677 (mt) REVERT: K 210 MET cc_start: 0.7273 (ppp) cc_final: 0.7059 (ppp) REVERT: K 211 MET cc_start: -0.0037 (ttp) cc_final: -0.0402 (ttm) REVERT: K 326 MET cc_start: 0.6049 (tpt) cc_final: 0.5561 (tpp) REVERT: M 158 MET cc_start: 0.7472 (mmp) cc_final: 0.7114 (mmm) REVERT: M 210 MET cc_start: 0.2573 (ppp) cc_final: 0.1741 (ptm) REVERT: M 211 MET cc_start: -0.0564 (ttm) cc_final: -0.1007 (ttt) REVERT: P 326 MET cc_start: 0.7366 (mmp) cc_final: 0.7151 (mmp) REVERT: Q 243 MET cc_start: 0.4705 (ppp) cc_final: 0.4493 (ttt) REVERT: R 211 MET cc_start: -0.0059 (ttm) cc_final: -0.0363 (ptm) REVERT: S 34 ASN cc_start: 0.5592 (p0) cc_final: 0.5351 (p0) REVERT: S 243 MET cc_start: 0.6299 (mmt) cc_final: 0.5607 (tmm) REVERT: T 306 ARG cc_start: 0.2298 (mmm160) cc_final: 0.1881 (tpt170) outliers start: 1 outliers final: 0 residues processed: 160 average time/residue: 0.5088 time to fit residues: 136.6444 Evaluate side-chains 124 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 4.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 4 optimal weight: 9.9990 chunk 18 optimal weight: 3.9990 chunk 324 optimal weight: 30.0000 chunk 54 optimal weight: 3.9990 chunk 265 optimal weight: 9.9990 chunk 333 optimal weight: 50.0000 chunk 146 optimal weight: 20.0000 chunk 279 optimal weight: 8.9990 chunk 366 optimal weight: 7.9990 chunk 167 optimal weight: 6.9990 chunk 6 optimal weight: 0.9980 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 244 HIS ** L 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 267 ASN ** R 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.059097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.039983 restraints weight = 409585.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 72)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.041260 restraints weight = 206447.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.042061 restraints weight = 129609.947| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.6443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 34066 Z= 0.178 Angle : 0.578 9.808 47270 Z= 0.322 Chirality : 0.039 0.186 5415 Planarity : 0.004 0.055 5012 Dihedral : 25.194 100.248 7175 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.14), residues: 3380 helix: 1.02 (0.12), residues: 1747 sheet: 0.26 (0.23), residues: 490 loop : -0.20 (0.18), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS F 75 PHE 0.017 0.002 PHE H 65 TYR 0.026 0.002 TYR F 98 ARG 0.010 0.000 ARG D 33 Details of bonding type rmsd hydrogen bonds : bond 0.04890 ( 1711) hydrogen bonds : angle 4.17132 ( 4679) covalent geometry : bond 0.00380 (34066) covalent geometry : angle 0.57816 (47270) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 3.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 ARG cc_start: 0.9009 (tmm160) cc_final: 0.8483 (ttp80) REVERT: D 62 MET cc_start: 0.9495 (mmm) cc_final: 0.9162 (mmm) REVERT: E 94 GLU cc_start: 0.9293 (tp30) cc_final: 0.8865 (tp30) REVERT: E 119 ILE cc_start: 0.9080 (pt) cc_final: 0.8861 (pt) REVERT: E 120 MET cc_start: 0.8397 (mpp) cc_final: 0.8133 (mpp) REVERT: F 81 VAL cc_start: 0.9083 (t) cc_final: 0.8857 (t) REVERT: G 91 GLU cc_start: 0.8904 (pp20) cc_final: 0.8495 (tm-30) REVERT: H 64 SER cc_start: 0.9506 (m) cc_final: 0.9279 (p) REVERT: K 211 MET cc_start: 0.0025 (ttp) cc_final: -0.0205 (ttm) REVERT: K 326 MET cc_start: 0.6297 (tpt) cc_final: 0.5808 (tpp) REVERT: M 158 MET cc_start: 0.6367 (mmp) cc_final: 0.5967 (mmm) REVERT: M 210 MET cc_start: 0.3736 (ppp) cc_final: 0.3312 (ptt) REVERT: P 326 MET cc_start: 0.6198 (mmp) cc_final: 0.5984 (mmp) REVERT: R 211 MET cc_start: 0.1412 (ttm) cc_final: 0.1189 (ttt) REVERT: S 243 MET cc_start: 0.6220 (mmt) cc_final: 0.5728 (tmm) REVERT: T 306 ARG cc_start: 0.2378 (mmm160) cc_final: 0.1881 (tpt170) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.4193 time to fit residues: 112.6470 Evaluate side-chains 122 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 3.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 308 optimal weight: 20.0000 chunk 118 optimal weight: 20.0000 chunk 9 optimal weight: 6.9990 chunk 310 optimal weight: 3.9990 chunk 250 optimal weight: 10.0000 chunk 130 optimal weight: 40.0000 chunk 207 optimal weight: 20.0000 chunk 315 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 233 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN E 108 ASN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 244 HIS ** M 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 244 HIS ** P 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.058816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.039876 restraints weight = 410761.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.041169 restraints weight = 205857.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 75)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.041972 restraints weight = 128849.721| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.6833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 34066 Z= 0.170 Angle : 0.563 9.108 47270 Z= 0.314 Chirality : 0.039 0.150 5415 Planarity : 0.004 0.075 5012 Dihedral : 25.041 101.187 7175 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.14), residues: 3380 helix: 1.17 (0.12), residues: 1747 sheet: 0.60 (0.27), residues: 370 loop : -0.53 (0.17), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.001 HIS M 244 PHE 0.022 0.001 PHE H 65 TYR 0.033 0.002 TYR H 83 ARG 0.004 0.000 ARG E 129 Details of bonding type rmsd hydrogen bonds : bond 0.04800 ( 1711) hydrogen bonds : angle 4.05379 ( 4679) covalent geometry : bond 0.00364 (34066) covalent geometry : angle 0.56335 (47270) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 3.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8250 (mmm) cc_final: 0.7846 (mmm) REVERT: A 125 GLN cc_start: 0.9181 (mp10) cc_final: 0.8851 (mm110) REVERT: D 62 MET cc_start: 0.9490 (mmm) cc_final: 0.9208 (mmm) REVERT: E 94 GLU cc_start: 0.9259 (tp30) cc_final: 0.8834 (tp30) REVERT: E 119 ILE cc_start: 0.9104 (pt) cc_final: 0.8823 (pt) REVERT: E 120 MET cc_start: 0.8395 (mpp) cc_final: 0.8080 (mpp) REVERT: G 56 GLU cc_start: 0.8697 (mm-30) cc_final: 0.8399 (mm-30) REVERT: K 211 MET cc_start: -0.0042 (ttp) cc_final: -0.0270 (ttm) REVERT: K 326 MET cc_start: 0.6638 (tpt) cc_final: 0.6173 (tpp) REVERT: L 158 MET cc_start: 0.5668 (mmp) cc_final: 0.5023 (mmm) REVERT: M 158 MET cc_start: 0.6099 (mmp) cc_final: 0.5640 (mmm) REVERT: M 210 MET cc_start: 0.3869 (ppp) cc_final: 0.3434 (ptm) REVERT: P 210 MET cc_start: 0.0568 (ppp) cc_final: 0.0205 (ppp) REVERT: P 326 MET cc_start: 0.6159 (mmp) cc_final: 0.5953 (mmp) REVERT: Q 211 MET cc_start: 0.3179 (tpp) cc_final: 0.2959 (tpp) REVERT: R 211 MET cc_start: 0.1400 (ttm) cc_final: 0.1166 (ttt) REVERT: S 243 MET cc_start: 0.6230 (mmt) cc_final: 0.5735 (tmm) REVERT: T 306 ARG cc_start: 0.2358 (mmm160) cc_final: 0.1811 (tpt170) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.4889 time to fit residues: 124.7463 Evaluate side-chains 118 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 4.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 77 optimal weight: 8.9990 chunk 242 optimal weight: 20.0000 chunk 197 optimal weight: 8.9990 chunk 221 optimal weight: 7.9990 chunk 88 optimal weight: 10.0000 chunk 270 optimal weight: 8.9990 chunk 213 optimal weight: 50.0000 chunk 41 optimal weight: 0.9980 chunk 289 optimal weight: 10.0000 chunk 44 optimal weight: 0.3980 chunk 284 optimal weight: 40.0000 overall best weight: 5.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 109 HIS E 108 ASN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 244 HIS ** O 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.057799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.042747 restraints weight = 381324.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.041938 restraints weight = 321054.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.041763 restraints weight = 275561.252| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.7424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 34066 Z= 0.202 Angle : 0.599 9.202 47270 Z= 0.332 Chirality : 0.040 0.177 5415 Planarity : 0.004 0.067 5012 Dihedral : 25.194 104.083 7175 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 17.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.14), residues: 3380 helix: 1.04 (0.12), residues: 1751 sheet: 0.49 (0.27), residues: 378 loop : -0.55 (0.17), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS B 75 PHE 0.020 0.002 PHE E 104 TYR 0.029 0.002 TYR H 40 ARG 0.009 0.001 ARG E 128 Details of bonding type rmsd hydrogen bonds : bond 0.05670 ( 1711) hydrogen bonds : angle 4.16539 ( 4679) covalent geometry : bond 0.00435 (34066) covalent geometry : angle 0.59922 (47270) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 3.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8147 (mmm) cc_final: 0.7756 (mmm) REVERT: B 97 LEU cc_start: 0.9690 (tp) cc_final: 0.9474 (tp) REVERT: D 62 MET cc_start: 0.9361 (mmm) cc_final: 0.8922 (mmm) REVERT: E 94 GLU cc_start: 0.9113 (tp30) cc_final: 0.8719 (tp30) REVERT: E 119 ILE cc_start: 0.8983 (pt) cc_final: 0.8610 (pt) REVERT: G 38 ASN cc_start: 0.8860 (m-40) cc_final: 0.8548 (p0) REVERT: G 56 GLU cc_start: 0.8575 (mm-30) cc_final: 0.8303 (mm-30) REVERT: G 91 GLU cc_start: 0.8948 (pp20) cc_final: 0.8544 (tm-30) REVERT: K 210 MET cc_start: 0.7364 (ppp) cc_final: 0.7077 (ppp) REVERT: K 211 MET cc_start: -0.0062 (ttp) cc_final: -0.0421 (ttm) REVERT: K 326 MET cc_start: 0.6760 (tpt) cc_final: 0.6370 (tpp) REVERT: M 158 MET cc_start: 0.7341 (mmp) cc_final: 0.6682 (mmm) REVERT: M 210 MET cc_start: 0.2810 (ppp) cc_final: 0.1837 (ptt) REVERT: M 211 MET cc_start: -0.1442 (ttt) cc_final: -0.1817 (ttt) REVERT: P 326 MET cc_start: 0.6693 (mmp) cc_final: 0.6315 (mmp) REVERT: S 34 ASN cc_start: 0.5344 (p0) cc_final: 0.5112 (p0) REVERT: S 243 MET cc_start: 0.6357 (mmt) cc_final: 0.5649 (tmm) REVERT: T 211 MET cc_start: -0.2426 (ttm) cc_final: -0.2714 (ttm) REVERT: T 306 ARG cc_start: 0.2266 (mmm160) cc_final: 0.1601 (tpt170) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.4214 time to fit residues: 103.4317 Evaluate side-chains 116 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 3.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 42 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 321 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 200 optimal weight: 20.0000 chunk 179 optimal weight: 7.9990 chunk 299 optimal weight: 6.9990 chunk 162 optimal weight: 30.0000 chunk 211 optimal weight: 50.0000 chunk 220 optimal weight: 7.9990 chunk 49 optimal weight: 0.9980 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 108 ASN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 62 ASN ** L 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.058162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.043037 restraints weight = 375981.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.042029 restraints weight = 326147.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.042000 restraints weight = 266647.266| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.7645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 34066 Z= 0.166 Angle : 0.569 8.339 47270 Z= 0.315 Chirality : 0.038 0.148 5415 Planarity : 0.004 0.061 5012 Dihedral : 25.032 103.245 7175 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.14), residues: 3380 helix: 1.18 (0.12), residues: 1749 sheet: 0.41 (0.27), residues: 380 loop : -0.52 (0.18), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS B 75 PHE 0.020 0.001 PHE H 65 TYR 0.019 0.002 TYR F 98 ARG 0.007 0.000 ARG R 241 Details of bonding type rmsd hydrogen bonds : bond 0.04634 ( 1711) hydrogen bonds : angle 4.02599 ( 4679) covalent geometry : bond 0.00357 (34066) covalent geometry : angle 0.56914 (47270) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 3.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8186 (mmm) cc_final: 0.7741 (mmm) REVERT: D 62 MET cc_start: 0.9376 (mmm) cc_final: 0.9061 (mmm) REVERT: E 94 GLU cc_start: 0.9170 (tp30) cc_final: 0.8811 (tp30) REVERT: E 119 ILE cc_start: 0.8843 (pt) cc_final: 0.8639 (pt) REVERT: G 38 ASN cc_start: 0.8889 (m-40) cc_final: 0.8629 (p0) REVERT: G 56 GLU cc_start: 0.8557 (mm-30) cc_final: 0.8325 (mm-30) REVERT: G 91 GLU cc_start: 0.8925 (pp20) cc_final: 0.8518 (tm-30) REVERT: K 210 MET cc_start: 0.7538 (ppp) cc_final: 0.7219 (ppp) REVERT: K 211 MET cc_start: -0.0164 (ttp) cc_final: -0.0515 (ttm) REVERT: K 326 MET cc_start: 0.6715 (tpt) cc_final: 0.6342 (tpp) REVERT: L 158 MET cc_start: 0.4576 (mmt) cc_final: 0.3381 (mmt) REVERT: M 158 MET cc_start: 0.7143 (mmp) cc_final: 0.6542 (mmm) REVERT: M 210 MET cc_start: 0.3224 (ppp) cc_final: 0.2327 (ptt) REVERT: M 211 MET cc_start: -0.1559 (ttt) cc_final: -0.1881 (ttt) REVERT: P 326 MET cc_start: 0.6797 (mmp) cc_final: 0.6451 (mmp) REVERT: R 125 MET cc_start: 0.7632 (pmm) cc_final: 0.7410 (pmm) REVERT: S 243 MET cc_start: 0.6437 (mmt) cc_final: 0.5681 (tmm) REVERT: T 306 ARG cc_start: 0.2485 (mmm160) cc_final: 0.1788 (tpt170) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.4159 time to fit residues: 99.8659 Evaluate side-chains 117 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 3.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 95 optimal weight: 7.9990 chunk 145 optimal weight: 6.9990 chunk 244 optimal weight: 7.9990 chunk 167 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 39 optimal weight: 6.9990 chunk 203 optimal weight: 8.9990 chunk 199 optimal weight: 8.9990 chunk 300 optimal weight: 50.0000 chunk 29 optimal weight: 7.9990 chunk 237 optimal weight: 10.0000 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 108 ASN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 330 ASN ** M 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 101 GLN ** P 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.057744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.042077 restraints weight = 377135.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.041451 restraints weight = 254442.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.041961 restraints weight = 182934.398| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.8031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 34066 Z= 0.183 Angle : 0.584 9.089 47270 Z= 0.323 Chirality : 0.039 0.162 5415 Planarity : 0.004 0.062 5012 Dihedral : 25.084 104.802 7175 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.14), residues: 3380 helix: 1.17 (0.12), residues: 1752 sheet: 0.32 (0.27), residues: 380 loop : -0.52 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS B 75 PHE 0.022 0.002 PHE H 65 TYR 0.021 0.002 TYR H 40 ARG 0.005 0.000 ARG N 247 Details of bonding type rmsd hydrogen bonds : bond 0.05229 ( 1711) hydrogen bonds : angle 4.06078 ( 4679) covalent geometry : bond 0.00393 (34066) covalent geometry : angle 0.58381 (47270) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 3.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8063 (mmm) cc_final: 0.7644 (mmm) REVERT: D 62 MET cc_start: 0.9197 (mmm) cc_final: 0.8863 (mmm) REVERT: E 94 GLU cc_start: 0.8975 (tp30) cc_final: 0.8603 (tp30) REVERT: E 119 ILE cc_start: 0.8936 (pt) cc_final: 0.8730 (pt) REVERT: G 56 GLU cc_start: 0.8659 (mm-30) cc_final: 0.8364 (mm-30) REVERT: G 91 GLU cc_start: 0.8930 (pp20) cc_final: 0.8509 (tm-30) REVERT: H 59 MET cc_start: 0.8834 (ttm) cc_final: 0.8550 (tpp) REVERT: K 210 MET cc_start: 0.7687 (ppp) cc_final: 0.7423 (ppp) REVERT: K 211 MET cc_start: -0.0244 (ttp) cc_final: -0.0570 (ttm) REVERT: K 326 MET cc_start: 0.6814 (tpt) cc_final: 0.6348 (tpp) REVERT: L 158 MET cc_start: 0.4743 (mmt) cc_final: 0.3747 (mmt) REVERT: M 158 MET cc_start: 0.7348 (mmp) cc_final: 0.6650 (mmm) REVERT: M 210 MET cc_start: 0.3829 (ppp) cc_final: 0.3135 (ptt) REVERT: M 211 MET cc_start: -0.1120 (ttt) cc_final: -0.1338 (ttt) REVERT: O 326 MET cc_start: 0.5995 (tpt) cc_final: 0.5630 (tpp) REVERT: P 326 MET cc_start: 0.6722 (mmp) cc_final: 0.6366 (mmp) REVERT: R 125 MET cc_start: 0.7608 (pmm) cc_final: 0.7372 (pmm) REVERT: S 243 MET cc_start: 0.6478 (mmt) cc_final: 0.5691 (tmm) REVERT: T 306 ARG cc_start: 0.2424 (mmm160) cc_final: 0.1769 (tpt170) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.4197 time to fit residues: 98.6022 Evaluate side-chains 116 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 3.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 33 optimal weight: 1.9990 chunk 258 optimal weight: 0.2980 chunk 77 optimal weight: 8.9990 chunk 44 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 362 optimal weight: 50.0000 chunk 123 optimal weight: 20.0000 chunk 166 optimal weight: 0.9990 chunk 79 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 163 optimal weight: 30.0000 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 108 ASN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 200 GLN O 188 ASN P 145 GLN P 188 ASN ** Q 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.058995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.044927 restraints weight = 374982.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.044416 restraints weight = 266807.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.044565 restraints weight = 214242.375| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.8103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 34066 Z= 0.128 Angle : 0.537 8.815 47270 Z= 0.298 Chirality : 0.038 0.170 5415 Planarity : 0.004 0.060 5012 Dihedral : 24.771 101.756 7175 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.15), residues: 3380 helix: 1.38 (0.12), residues: 1799 sheet: 0.34 (0.27), residues: 380 loop : -0.59 (0.18), residues: 1201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS F 75 PHE 0.021 0.001 PHE H 65 TYR 0.019 0.001 TYR F 98 ARG 0.005 0.000 ARG E 116 Details of bonding type rmsd hydrogen bonds : bond 0.03869 ( 1711) hydrogen bonds : angle 3.78791 ( 4679) covalent geometry : bond 0.00271 (34066) covalent geometry : angle 0.53724 (47270) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 3.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.9538 (mmm) cc_final: 0.9191 (mmp) REVERT: A 120 MET cc_start: 0.8131 (mmm) cc_final: 0.7716 (mmm) REVERT: E 92 LEU cc_start: 0.9554 (mt) cc_final: 0.9132 (tt) REVERT: E 94 GLU cc_start: 0.8824 (tp30) cc_final: 0.8458 (tp30) REVERT: E 120 MET cc_start: 0.8286 (mpp) cc_final: 0.8001 (mpp) REVERT: G 56 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8278 (mm-30) REVERT: G 91 GLU cc_start: 0.8900 (pp20) cc_final: 0.8436 (tm-30) REVERT: H 59 MET cc_start: 0.8632 (ttm) cc_final: 0.8262 (tpp) REVERT: K 158 MET cc_start: 0.0352 (mmm) cc_final: -0.0137 (mmm) REVERT: K 210 MET cc_start: 0.7785 (ppp) cc_final: 0.7466 (ppp) REVERT: K 211 MET cc_start: -0.0177 (ttp) cc_final: -0.0433 (ttm) REVERT: K 326 MET cc_start: 0.6690 (tpt) cc_final: 0.6305 (tpp) REVERT: L 158 MET cc_start: 0.4134 (mmt) cc_final: 0.3043 (mmt) REVERT: M 158 MET cc_start: 0.7248 (mmp) cc_final: 0.6623 (mmm) REVERT: M 210 MET cc_start: 0.3820 (ppp) cc_final: 0.2869 (ptt) REVERT: M 211 MET cc_start: -0.1562 (ttt) cc_final: -0.1776 (ttt) REVERT: P 326 MET cc_start: 0.7121 (mmp) cc_final: 0.6775 (mmp) REVERT: R 125 MET cc_start: 0.7569 (pmm) cc_final: 0.7325 (pmm) REVERT: S 243 MET cc_start: 0.6364 (mmt) cc_final: 0.5503 (tmm) REVERT: T 306 ARG cc_start: 0.2471 (mmm160) cc_final: 0.1780 (tpt170) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.4090 time to fit residues: 100.9901 Evaluate side-chains 117 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 3.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 148 optimal weight: 30.0000 chunk 92 optimal weight: 10.0000 chunk 272 optimal weight: 10.0000 chunk 66 optimal weight: 8.9990 chunk 131 optimal weight: 8.9990 chunk 67 optimal weight: 0.9990 chunk 306 optimal weight: 30.0000 chunk 309 optimal weight: 20.0000 chunk 318 optimal weight: 0.5980 chunk 42 optimal weight: 9.9990 chunk 156 optimal weight: 9.9990 overall best weight: 5.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 108 ASN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.057220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.042459 restraints weight = 379928.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.041959 restraints weight = 315809.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.041898 restraints weight = 246622.711| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.8461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 34066 Z= 0.206 Angle : 0.602 8.784 47270 Z= 0.333 Chirality : 0.040 0.152 5415 Planarity : 0.004 0.062 5012 Dihedral : 25.073 105.595 7175 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 18.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.14), residues: 3380 helix: 1.25 (0.12), residues: 1752 sheet: 0.26 (0.27), residues: 380 loop : -0.50 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.001 HIS F 75 PHE 0.017 0.002 PHE H 65 TYR 0.022 0.002 TYR H 40 ARG 0.005 0.000 ARG M 170 Details of bonding type rmsd hydrogen bonds : bond 0.05679 ( 1711) hydrogen bonds : angle 4.13920 ( 4679) covalent geometry : bond 0.00444 (34066) covalent geometry : angle 0.60208 (47270) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11150.26 seconds wall clock time: 201 minutes 3.68 seconds (12063.68 seconds total)